Those cones are tethers showing side chain connections to the ribbon.  See this post for hiding them.

    https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/RY4ECKYMZRAEC3TZCE327CIVHAVHCW2L/

  Tom

On Jul 3, 2026, at 9:31 PM, Francisco via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:



open /path/to/foo.pdb
hide atoms
select (#1/A:15,35,52,101,129 :< 5) & protein
show sel atoms
cartoon suppressBackboneDisplay false
and then zooming into the carboxy-term at L129

How do I hide the ghost bonds? (i.e. the bond between OXT and the end of the tube, which is not an atom, and the bond between the C atom and also the end of the tube..)

Thanks

<Screenshot From 2026-07-03 09-56-23.png>

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